Next Generation Sequencing for the Food Industry
More and more, it is becoming true that nothing drives detection and prevention of food-borne illness than technology (and, of course, with advancements in detection come potential increases in exposure to legal liability). No technological advancement may be more significant than Next Generation Sequencing ("Next Gen Sequencing").
I've recently had the opportunity to spend time learning about Next Gen Sequencing
with Dr. Andrew Benson, a genetic microbiologist at the University of Nebraska’s Department of Food Science and Technology. Dr. Benson has received large research grants to harness the power of Next Gen sequencing. If you’re interested in the field, take a look at this short video, where Dr. Benson explains the technology, and check out the information on the CAGE (Core for Applied Genomics and Ecology) website.
As described on the CAGE website, this Next Gen technology “allows a single machine to accomplish in 48 hours what used to take an entire room full of machines and an army of
staff a month to achieve.”
Dr. Benson and others at CAGE explain further that:
Having such a powerful diagnostic technique now challenges us to rethink completely how we might go about risk assessment. Instead of looking for a single “indicator organism” in a food sample, we can now look at the entire population of microorganisms in a food sample and ask if the community of organisms present is the expected species that normally occupy that food or if the sample contains numbers of unexpected species, and in particular those species that are unique to fecal or soil environments. Thus, our assessment of “risk” is now based on the entire population, including the most abundant species of fecal and soil communities. Because our assessment is based on the entire composition, multiple species that are unique to feces or soil can be used in the determination, making the assessment much more accurate and robust. Moreover, the assessment is not limited to “risk” as we can also determine if the microbial community in a food sample has shifted toward spoilage (which gives us shelf-life predictions) or is consistent with “good” organoleptic properties of the food. The list of applications goes on and on.
Discoveries using this technology are happening at astonishing speed. PFGE testing, now considered the "gold standard" and generic E.coli testing may soon seem old fashioned and crude.
What to Do When the Investigators Knock . . .
This week brought news of yet another nationwide Salmonella outbreak from a source not yet identified by government regulators. The last time we had a nationwide Salmonella outbreak for an extended period of time without identification of a definitive source the federal government initially singled out tomatoes imported from Mexico (a huge array of products). In that case, the government was wrong and wreaked financial havoc on many farmers and businesses.
So far, in the current outbreak, nothing more specific than “poultry, eggs and cheese” have been identified as possible sources. Last year’s outbreak involved Salmonella Saintpaul whereas the current outbreak is Salmonella Typhimurium, which is more commonly associated with poultry, eggs and cheese, but could come from almost anything.
That a source has yet to be identified to the media doesn’t mean that state and federal officials aren’t zeroing in on possible sources. Restaurant owners, retailers and food manufacturers should be ready for the regulators when they come knocking.
In the past, I’ve had clients who were worked over aggressively by regulators (especially federal officials) who were investigating a large, nationwide outbreak with an uncertain cause. These officials face enormous pressure from those in Washington and from the public. Federal officials can make demands that threaten an entire business. They can demand credit card receipts, contact information for customers, personal employee information, shutdown of the business and more. Noncompliance might mean the officials will go to the press and advertise that the business is a target of the investigation. Unlike local health officials, who are usually vested in the well-being of local food producers under their jurisdiction, federal officials may care only about the investigation and nothing else.
Any food business should implement its crisis response team the minute it suspects it could be targeted in an investigation like the one that is currently ongoing. Specialists in food safety and foodborne illness investigations, genetic microbiologists, public relations experts, accountants, quality assurance personnel, purchasing personnel and lawyers should be lined up and ready to go. Events may unfold quickly for your business (over the course of a day or even a morning). Everything needs to be done at that moment to assist a business in navigating what may appear to be an impossible crisis.
Dramatic Shift in Plaintiffs' Burden of Proof for Food-Borne Illness Claims?
A California Court of Appeal panel recently issued a lengthy decision in Sarti v. Salt Creek Ltd. (2008 WL 5006537) reversing a trial court’s grant of judgment notwithstanding the verdict (JNOV) in a food-borne illness case involving campylobacter. Sarti is alarming. The California court substantially lightened the plaintiff’s burden of proof by requiring her to come forth with only enough evidence to “infer” a causational nexus between her illness and the defendant’s food. Close examination of the facts in Sarti reveals that the plaintiff in that case may not have proven anything to establish a causational nexus.
Sarti involves a woman who allegedly became ill with campylobacter the morning after she consumed a raw ahi tuna appetizer at the defendant’s restaurant. According to the Cleveland Clinic, campylobacter has a two- to five-day incubation period. The court does not explain in its decision what, if any, expert testimony was introduced to explain how the incubation period was compatible with the plaintiff’s allegations. Without expert testimony explaining away the apparent insurmountable problem of the incubation period, plaintiff's case should fail as a matter of law. In other words, the plaintiff’s case should never have survived summary judgment.
Not only does the incubation period make the plaintiff’s claim problematic, but other sources of contamination were identified. For example, the court explained that “Sarti herself worked as a supermarket checker the day she became ill, and could, at least in theory, have picked up campylobacter from a leaking bag of raw chicken she might have scanned.”
The plaintiff’s expert offered some theories about how the tuna dish could have become cross-contaminated. According to the health department, “Wipe down rags were not being sanitized between in wiping down surfaces. There was also an insufficient amount of sanitizer in the dishwasher. Chicken tongs were sometimes uses for other food. Raw vegetables were stored under ‘raw meat.’”
The Sarti decision does not indicate whether the plaintiff’s expert could identify any of these theories as more or less likely than sources having nothing to do with the defendant’s restaurant (and, in fact, given the incompatibility of the incubation period, one would think that the defendant’s restaurant should be discounted as the cause). The court does not explain how a reasonable jury could conclude that the plaintiff’s cross-contamination theories were any more likely than the alternative theories for the plaintiff’s illness.
Instead of citing evidence or expert testimony, the Sarti court relies upon a series of food-borne illness cases in California going back nearly a century that address issues of causation. All of the cases relied upon predate DNA serotyping of bacteria, pulsed-field gel electrophoresis, modern techniques of epidemiology, microbiology and medicine. Sarti is seemingly a reversion to the dark ages of food science when it was reasonable to believe that the last thing a person ate is what made the person sick. The Sarti court ignores the science and believes that a jury should be able to do the same.
